Weekly Brief, 22 August 2022

This week's highlights

Impact evaluation at ELIXIR

As a publicly funded organisation, it is important that ELIXIR provides evidence of its public value. A multi-pronged approach has been taken to building capacity through many years of ELIXIR funded work, including peer mentoring, formal training by experts, knowledge exchange events and the provision of tools and worked examples.

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Fifth Show & Tell: Impact of international activities on national level

07 October 2022 | 10am CEST

Johanna Trnroos from ELIXIR Finland will present on Impact of international activities on the national level. This event is part of the ELIXIR Strategic Implementation Study on Impact, in collaboration with ELIXIR-CONVERGE WP4. All participants are welcome to join, especially those involved in ELIXIR and interested in impact evaluation.

Register now

Recommended reads

Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression

An ELIXIR-EXCELERATE & eTRANSAFE paper

Understanding the molecular basis of major depression is critical for identifying new potential biomarkers and drug targets to alleviate its burden on society. Leveraging available GWAS data and functional genomic tools to assess regulatory variation could help explain the role of major depression-associated genetic variants in disease pathogenesis. The authors conducted a fine-mapping analysis of genetic variants associated with major depression and applied a pipeline focused on gene expression regulation by cis-eQTL colocalization analysis and alteration of transcription factor binding sites. The fine-mapping process uncovered putative causally associated variants whose proximal genes were linked with major depression pathophysiology. Overall, the pipeline could prioritize putative causal genetic variants in major depression. The presented approach enabled the proposal of mechanistic hypotheses of these genetic variants and their role in disease pathogenesis.

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The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

An ELIXIR-FR paper

Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the Ocean Gene Atlas (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available online.


Read more

Updates from Nodes

BioSB bioinformatics and systems biology courses

Five BioSB bioinformatics and systems biology courses are now open for registration, read more and register online

• Machine Learning (Fundamental)
  26-30 September 2022 | Amsterdam, Netherlands

• Algorithms for Genomics (Advanced)
  10-14 October 2022 | Delft, Netherlands

• Computational Metagenomics
  10-12 October 2022 | Wageningen, Netherlands

• Single cell Analysis
  10-14 October 2022 | Leiden, Netherlands

• Constraint-based modeling: Introduction and advanced topics
  13-17 February 2023 | Wageningen, Netherlands

New chair of the DMP Common Standards working group of RDA

Marek Suchnek from ELIXIR-CZ took over the position of chair of the DMP Common Standards working group of the Research Data Alliance. Marek Suchnek is part of the DS Wizard team and has been actively contributing to the activities of this group. A big thank you to Paul Walk who is stepping down from being the chair.

Updates from Platforms

Compute Platform annual F2F event summary report

The Compute Platform held its annual F2F event in Berlin, Germany in April 2022. The event was co-hosted by the ELIXIR-DE Node and included a diverse range of topics such as hybrid cloud, containers, AAI and European human data projects.

Read the full event summary report on Zenodo

Updates from Communities

ELIXIR Metabolomics Community: Call for two co-leads

Deadline: 26 August 2022

The ELIXIR Metabolomics Community is looking for two new co-leads to join the current Community leadership team. The Community is opening a self-nomination process. Candidates should submit a short statement of their background and what they believe they will bring to the role.

For any questions or nominations, please contact Katharina Heil
More information

Updates from Focus Groups

ELIXIR Europe landscape analysis of RDA involvement

Deadline: 19 September 2022

Is the Research Data Alliance (RDA) a new acronym to you? Or are you already an RDA pro and heavily engaged in RDA activities? The ELIXIR RDA Activities Focus Group are conducting a landscape analysis survey of ELIXIR members and their extent of engagement in the RDA. It takes approximately 5 minutes to complete and contains useful links and information on the RDA and Focus Group throughout.

Fill out the survey

Updates from Other Initiatives

The Europe Biobank Week Roadshow on Quality
19-20 September 2022 | Regensburg, Germany

The Europe Biobank Week Roadshow on Paediatric Biobanking
13-14 October 2022 | Rome, Italy

The Nordic Biobank Conference
6-8 September 2022 | Gothenburg, Sweden

EJP-RD BYOOD Workshop

17-18 November 2022 | Nijmegen, Netherlands

The Bring Your Own Omics Data workshop (BYOOD) workshop aims to help you optimising and integrating your omics data, initiating network analysis, and continue collaborations with the data analysis team.

Please complete the pre-registration form by the 2 September 2022

GA4GH 10th Plenary

22-23 September 2022 | Barcelona, Spain

Join the Global Alliance for Genomics and Health (GA4GH) 10th Plenary in Barcelona, co-hosted by Bioinformatics Barcelona, the meeting unites the genomics and health community for two days of conversation on data sharing. Attendees will have the opportunity to learn about GA4GHs technical standards, policy frameworks, and implementations.

Sign up now

Register for eRImote workshop

21 & 22 September 2022 | Virutal

The first workshop of the eRImote project will focus on remote training for RI users and staff, as well as exploring the impact of remote/digital service provision on user interaction and networking.

Register now

Registration for the first Colloquium on Bioinformatics Learning, Education and Training (CoBLET) opens

11-14 October 2022 | Hybrid - Istanbul, Turkey

The first Colloquium on Bioinformatics Learning, Education and Training (CoBLET) will focus on thematic discussions targeting education and training in bioinformatics. It will be held in conjunction with the 11th Annual General Meeting of GOBLET.

More information

Upcoming ELIXIR events & webinars

ELIXIR Training Courses & Webinars

The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes. For more, visit TeSS portal

ELIXIR Webinar: Exploring structural and functional annotations of IDPs with DisProt
23 August 2022 | 15:00 CEST

ELIXIR Events and Conference

ELIXIR Innovation and SME Forum: Data driven innovation in healthcare diagnostics
22 September 2022 | 10:00 to 19:00 CEST | Barcelona, Spain

ELIXIR Bioinformatics Industry Forum: Enabling Ecosystems for Machine Learning in the Life Sciences
11 October 2022 | 10:00 to 16:00 CEST | London, UK

BioHackathon Europe

7-11 November 2022 | Paris, France

Job vacancies

All vacancies are also published on the ELIXIR website (also including those from industry). If you need our help communicating your new open positions, you can submit a job advertisement and it will automatically appear on our newsletters. Go to our vacancy page to submit a job
 

Senior Scientific Officer - Cancer Data

ELIXIR Hub

Project Manager Human Genomics Data

VIB

Team Leader - Health Data Research

Barcelona Supercomputing Center (BSC-CNS)

Software developer

VIB

Scientific Relations Manager (50-60%)

Institut Suisse de Bioinformatique